NBIS ID: SMS_6198
Report Version: 1.0
Request by: Mona N. Högberg ()
Principal Investigator: Mona N. Högberg ()
Organisation: SLU
NBIS Staff: Juliana Assis ()


1 Setup

## LIBRARIES
library("dada2")
library("devtools")
library("dplyr")
library("ggplot2")
library("microbiome")
library("phangorn") 
library("phyloseq") 
library("Rcpp")
library("reshape2")
library("tidyr")
library("vegan")
library("ShortRead")
library("Biostrings")
library("DECIPHER")
library("SensusR")
library("gplots")
library("gridExtra")
library("grid")
library("ggpubr")
library("reshape2")
library("reshape")
library("lulu")
library("ggrepel")
library("ggh4x")
library("RColorBrewer")
library("rITSx")
library("MicEco")

2 Version

1.0

  • Support Request
    Request sent by the user: Mona N. Högberg

3 Data

96 samples

  • Type of data

ITS amplicon

  • Data location rackham.uppmax.uu.se /proj/snic2022-22-352

  • Uppmax project ID SNIC 2022/22-352

  • NGI Project ID P9723

  • Database used Unite

4 Tools

NFCore-Ampliseq (Dada2)

#Sample Info
head(sample_info_tab)

5 Workflow

5.1 Replicates Evaluation

Alpha Diversity Plot comparing the Replicates A and B.

Quality control analysis using matched samples from 3 different Transects: A, B and C of the experiment and replicates samples on each Ecotype. Comparison of alpha diversity in technical replicates samples on all Ecotypes from each Transect. ASV richness and ASV Shannon diversity.

  • Beta Diversity Plot comparing the Replicates A and B.

* Beta Diversity Plot comparing the Replicates A and B.

Rarefaction

5.2 Main Analysis

  • Alpha Diversity Plot - A.

* Beta Diversity Plot - A.

* Beta Diversity Plot - B.

* Permutational analysis of variance

  • Relative abundance of the top 50 ASVs

6 Summary

Help is needed with running the “nfcore/ampliseq” pipeline developed at NGI for the analyses of fungal ITS1 amplicons, Illumina Miseq analysis NGI project ID P5953 (M.Hogberg_17_01_project summary from 2018-01-19 by Chuan Wang refers to P9723, >=Q30 (mean(SD), 70(2) (%), Sum Reads=15 650 000, Mean reads per sample 171 711, 1 pool of amplicons, 1 flowcell v3, PE 2x301bp (validated method), demultiplexing, quality control and raw data delivery on Uppmax (validated method). Agreement number M.Hogberg_16_01-20160826. Grus delivery project delivery 00654. Because my support application 2019-01-17 was rejected, I have collaborated with partners in US on this matter but all is extremely delayed for known reasons. I got some hope today when I read about the recently developed pipeline for fungal analyses! Unfortunately, I have no programming skills but have a BSc in Molecular Biology.

Short summary of the work.

7 Further Work

Further steps to be taken (if needed).

8 References

Relevant references for methods, tools etc.

9 Deliverables

Files delivered to the user with descriptions.

9.1 Directory

/data/processed/b/

8 directories, 18 files

Total size is XX GB.

10 Timeline

11 Practical Info

11.1 Data responsibility

The responsibility for data archiving lies with the PI of the project. We do not offer long-term storage or retrieval of data.

  • NBIS & Uppnex: We kindly ask that you remove the files from UPPMAX/UPPNEX. The main storage at UPPNEX is optimized for high-speed and parallel access, which makes it expensive and not the right place for longer time archiving. Please consider others by not taking up the expensive space. Please note that UPPMAX is a resource separate from the Bioinformatics Platform, administered by the Swedish National Infrastructure for Computing (SNIC) and SNIC-specifc project rules apply to all projects hosted at UPPMAX.
  • Sensitive data : Please note that special considerations may apply to the human-derived legally considered sensitive personal data. These should be handled according to specific laws and regulations as outlined e.g. here.
  • Long-term backup : We recommend asking your local IT for support with long-term data archiving. Also a newly established Data Office at SciLifeLab may be of help to discuss other options.

11.2 Acknowledgments

If you are presenting the results in a paper, at a workshop or conference, we kindly ask you to acknowledge us.

  • NBIS staff are encouraged to be co-authors when this is merited in accordance to the ethical recommendations for authorship, e.g. ICMJE recommendations. If applicable, please include Juliana, Assis Geraldo, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, NBIS, as co-author. In other cases, NBIS would be grateful if support by us is acknowledged in publications according to this example:

“Support by NBIS (National Bioinformatics Infrastructure Sweden) is gratefully acknowledged.”

“The computations were performed on resources provided by SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) under Project SNIC 2022-22-352.”

  • NGI : For publications based on data from NGI Sweden, NGI, SciLifeLab and UPPMAX should be acknowledged like so:

“The authors would like to acknowledge support from Science for Life Laboratory (SciLifeLab), the National Genomics Infrastructure (NGI), and Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) for providing assistance in massive parallel sequencing and computational infrastructure.”

12 Support Completion

You should soon be contacted by one of our managers with a request to close down the project in our internal system and for invoicing matters. If we do not hear from you within 30 days the project will be automatically closed and invoice sent. Again, we would like to remind you about data responsibility and acknowledgements, see sections: Data Responsibility and Acknowledgments.

You are welcome to come back to us with further data analysis request at any time via http://nbis.se/support/support.html.

Thank you for using NBIS.